Development and characterization of nuclear microsatellite markers for Eremanthus erythropappus and their transferability across related species

Abstract

Background: We developed simple sequence repeats (SSR) for Eremanthus erythropappus (DC.) MacLeish, an endangered tree species endemic to the Brazilian Savanna and Atlantic Forest biomes, and tested their transferability to two closely related Eremanthus species. Results: Using a genomic library enriched with tandem repeat motifs, we identified 16 primer pairs, and characterized them in two populations. Nine primers amplified the expected size fragments and seven SSRs were polymorphic, providing a total of 38 alleles and an average of 4.22 alleles per marker. The polymorphic information content (PIC) ranged from 0.44 to 0.94 with an average of 0.65. The average observed heterozygosity across all loci varied from 0.61 to 1.00. The observed (H O) and expected (H E) heterozygosity within the two populations varied from 0.65 to 1.00 and from 0.31 to 1.00, respectively. Conclusions: These newly developed SSR markers are a powerful tool for population genetic analyses and may be useful in studies on species ecology, evolution, and taxonomy.

Fine-scale analysis reveals a potential influence of forest management on the spatial genetic structure of Eremanthus erythropappus

“…DNA extraction was carried out using the CTAB protocol (Doyle and Doyle 1987), quantified using a NanoVue Plus™ spectrophotometer, and its purity checked using the A 260 /A 280 ratio. Noncorrelated microsatellite primers were used for the PCR process (Ere02, Ere03, Ere04, Ere07, Ere08 and Ere14) developed for E. erythropappus (Rocha et al 2020b) according to specific conditions (see supplementary Table S1). The total volume of each sample was 15.0 μL: approximately 30 ng of DNA was added to 12.0 μL of reaction mixture (3.33 mM IB Phoneutria buffer consisting of 100 mM Tris-HCl pH 8.4; 500 mM KCl, 1% Triton X-100, 15 mM MgCl 2 ), 1.5 mM MgCl 2 , 0.28 mM of each dNTP, 1 U Taq polymerase, 0.22 mM each primer (Forward and Reverse) and the final volume was achieved with ultrapure water.…”